Greetings from Japan! For those who may have been wondering, super-typhoon Hagibis caused no damage to my home, and my family is safe and sound. Around Japan, however, over 430,000 households are currently without electricity, including 148,000 in my prefecture. But tomorrow is another day, and Japan is an amazingly resilient country. People who’d like to know more are welcome to check out this Website.

Today’s post relates to an excellent one-hour movie on John Henry Newman (1801-1890), the Catholic Church’s newest saint (his canonization ceremony is on Sunday, October 13). The movie was created by Catholic theologian and author Bishop Robert Barron, founder of the Catholic ministerial organization Word on Fire. The movie, titled St. John Henry Newman: The Convert, may be viewed online here, but only until October 31. It is very professionally put together: the brilliant cinematography, combined with the uplifting music and Bishop Barron’s erudite narration, makes for thoroughly enjoyable viewing. The first half-hour deals with Newman’s life. at 30:54, Bishop Barron discusses Newman’s classic work, The Development of Christian Doctrine, elucidating its insights with limpid clarity in a segment which is well worth watching. At 40:00, the discussion switches to another work of Newman’s: The Idea of a University.

It has been a long time since my last post on this site. One reason for that is that I’ve been proofreading a forthcoming book (not by me), about which I shall say no more for now. Another reason is that I’ve been planning a talk which I hope to put up on Youtube next year. This is something I’ve never done before, so any technical, logistical and promotional advice would be greatly appreciated.

But the most interesting part for visitors to The Skeptical Zone, begins at 47:15, and relates to Newman’s masterpiece, The Grammar of Assent. In this work, Newman criticized the fixation philosophers have with the idea of certitude. Certitude, he argued, is the wrong starting point; the right starting point is assent. Bishop Barron, in his commentary, carefully explains the distinction Newman drew between the notional assent we give to abstract propositions (the example Barron gives is the proposition that slavery is wrong), and the real assent we give to concrete things (for example, that the reality of slavery, which I see here before me, is evil). Real assent affects the way we act and behave. Newman maintained that the ground of real assent in matters of religion is conscience, which he defined as “a certain keen sensibility, pleasant or painful … attendant on certain of our actions, which in consequence we call right or wrong”. Newman was struck by the fact that conscience is often likened to a voice. Through it we know that we please or offend a Person by our acts – in Newman’s words, “a Judge, holy, just, powerful, all-seeing.” The next segment, starting at 51:32 and lasting about four minutes, is the subject of this post: it relates to the assent which we give to a proposition. From here on, I’ll quote Bishop Barron’s own words, which I have transcribed below.

In a recent thread, commenter Eric Holloway links to an article in which he claims to have proven that halting oracles are logically possible.

The one-page article can be found here:

The Logical Possibility of Halting Oracles

I’ve taken a look at the article, and the proof contains a blatant circularity. That is, it assumes that halting oracles are possible in order to demonstrate that they are possible.

Eric’s proof depends on the construction of an infinite table (which he calls an ‘index’, for some reason) containing an entry for every possible finite Turing machine. The entry includes a specification of the machine in question and a “halting status” that indicates whether the machine halts or runs forever.

Another machine (the “search machine”) is set up that can search through the infinite table to find any particular finite state machine. If it finds a match, it returns the associated halting status. The search machine together with the infinite table thus constitute a halting oracle, according to Eric.

The problem is simple: To populate the infinite table, you need to know the halting status of each finite machine, and to get the halting status, you need a halting oracle. Eric thus assumes the logical possibility of a halting oracle in order to prove the logic possibility of a halting oracle.

It’s plainly circular.

There are additional problems with the article that we can discuss in the comment thread.

on another blog called pandas Thumb Joe Felsenstein directed readers to the 2019 evolution videos. i canned them, watch numerous summeries, and a few whole programs.

Added by moderator: This appears to be the Panda’s Thumb post that is being referenced. The videos appear to be HERE.

The only one i gave thumbs up to was by a dude called Bowen. It was called adaptative radiations. What the flock is going on?

I really like this as a creationist. He talks about flocks of specification that turns up everywhere now in the sees. they find, like in the cichlid fishes of africa, clusters/flocking of dozens of species from a parent one.

This is not what evolutionists should expect and Bowen suggests there must be some NEW evolutionary rule guiding this. He finds it everywhere.

The title is from a blog post by Brian Leiter. Leiter links to an article in the LA Review of books: Imitation and Extinction: The Case Against Reality. The article is written by Donald Hoffman.

We have discussed the general topic before, in several threads. So maybe this is a good time to revisit the topic.

Hoffman asks: “I see a green pear. Does the shape and color that I experience match the true shape and color of the real pear?”

My take is that there is no such thing as the “true shape and color of the pear.”

It is a common presumption, that there is an external standard of truth. Here, I mean “external to humans”. Truth is presumed to come from somewhere else. And our perceptual systems evolved to present us with what is true.

As I see it, this is backwards. Yes, our perceptions are mostly true. But this is not because perception is based on truth. Rather, it is because our human ideas of truth are based on what we perceive.

Open for discussion.

The methods of modern research involves dissecting and focusing in on finer and finer details. We would be forever blind to these finer details if it weren’t for instruments such as the microscope and the telescope. These tools allow specialists to focus in on the parts and gain a tremendous amount of knowledge in narrow fields.

But if researchers don’t look beyond these isolated islands of existence they will settle for a fragmented view of reality. And this causes problems for building theories about development and evolution of life. Researchers begin by looking at the parts to try to understand how they “build” bodies. Viewing things from this perspective it was expected that humans would have many more genes than turned out to be the case.. This is the type of error produced by this way of thinking Initially they did not understand the way in which the organism used its genes because they approached it from the wrong direction. Genes are in reality never isolated from the context of networks, cells and organisms.

Jaap van der Wal argues that we have become accustomed to thinking the human organism is made by a process of cells multiplication. But there is another more realistic way of thinking about it. From conception to adulthood a human being has always been a complete organism with a form and function suited to its environment. A machine is assembled from parts and it can only function as intended when all the parts are in place. Organisms are not like this. Where the organism is concerned the cell or cells of which it is composed serve the whole organism throughout its existence. It is not gradually built from parts. Machines are always built from the parts to the whole but organisms are never anything but complete wholes.

It is time to start paying more attention to how the whole determines the parts within it and luckily this view is becoming more prevalent.

I have committed the unpardonable sin of promoting ID as theology and arguing ID is not science. ID is the lineal descendant of Paley’s natural theology (as in contrast to “revealed theology”). I’ve publicly disputed the use of the 2nd Law of Thermodynamics as a general argument in favor of ID/Creation, and I’ve been mildly critical of the concept of specified complexity and its successors. I’ve suggested ID is most appropriately taught in college/seminary theology and philosophy departments. When I published a 2005 exchange between myself and Eugenie Scott of the NCSE regarding the appropriateness of ID being taught in college religion and philosophy departments, Eugenie was much kinder to me than some in the ID community who insist “ID is science.” See: Correspondence between Salvador Cordova and Dr. Eugenie Scott

To that end, in conjunction with university professors, deans of Christian and secular colleges (who are favorable to both Intelligent Design and belief in Special Creation), I’m helping build out the electronic component of courses that teach ID and concepts of Creationism for such venues.

In 2015, Winston Ewert, William Dembski and Robert Marks published a paper entitled Algorithmic Specified Complexity in the Game of Life.

The paper was a wreck. We examined it here at TSZ and found well over 20 substantive errors in it.

ID supporter Eric Holloway describes it as a “neat paper”. I describe it as an “abysmal mess”.

Eric has been touting the virtues of ASC here at TSZ, so now is a good time to reopen the discussion of this paper.

Intelligent Design advocates are still talking about CSI and determining the value of it.

CSI measures whether an event X is best explained by a chance hypothesis C, or some specification S.

So I’d like this thread to be a list of biological entities and the value of CSI that has been determined for each.

If no entries are made then I believe that would demonstrate that CSI might measure X Y or Z but it never actually has done so.

Out of interest, what is the CSI of a bacterial flagellum?

It is an embarrassment to be associated with the academy when pathological idiocy of this sort is published and cited in the same manner as genuine intellectual/scientific endeavor… What the hell is wrong with us? — Jordan Peterson, Tweet with link to paper

One can follow the hyperlink to see what Peterson was specifically talking about (I didn’t quote from the paper Peterson was criticizing since it was too vulgar). But more generally, in a recording (which might already be deleted from the net), Peterson praised the RealPeerReview twitter website that highlighted some of the publications of the academics which Peterson was likely also referring to when he used the phrase “pathological idiocy.”

Specifically, it looks like the genetic code is a LISP dialect.

Operon structure of genetic code:
– https://s3-us-west-2.amazonaws.com/courses-images/wp-content/uploads/sites/1094/2016/11/03164740/OSC_Microbio_11_07_Operon.jpg

LISP function structure:
– http://support.ircam.fr/docs/om/om6-manual/res/listprefix.png

Nested genes:
– https://player.slideplayer.com/31/9782148/data/images/img11.jpg

Nested LISP cons cells:
– https://www.tutorialspoint.com/lisp/images/treestructure.jpg

The Extinction of π

H/T Richardthughes at AtBC